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- PDB-4r5x: Structure of the m1 alanylaminopeptidase from malaria complexed w... -

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Basic information

Entry
Database: PDB / ID: 4r5x
TitleStructure of the m1 alanylaminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor
ComponentsM1 family aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / chloroplast / proteolysis / zinc ion binding ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / chloroplast / proteolysis / zinc ion binding / membrane / nucleus / cytoplasm
Similarity search - Function
Peptidase M1, alanyl aminopeptidase, C-terminal domain / Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like fold ...Peptidase M1, alanyl aminopeptidase, C-terminal domain / Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like fold / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-R5X / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum FcB1/Columbia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsDrinkwater, N. / Mcgowan, S.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Two-Pronged Attack: Dual Inhibition of Plasmodium falciparum M1 and M17 Metalloaminopeptidases by a Novel Series of Hydroxamic Acid-Based Inhibitors.
Authors: Mistry, S.N. / Drinkwater, N. / Ruggeri, C. / Sivaraman, K.K. / Loganathan, S. / Fletcher, S. / Drag, M. / Paiardini, A. / Avery, V.M. / Scammells, P.J. / McGowan, S.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M1 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,40213
Polymers105,2021
Non-polymers1,20012
Water15,205844
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.447, 109.066, 117.649
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein M1 family aminopeptidase / Pfa-M1


Mass: 105202.273 Da / Num. of mol.: 1 / Fragment: UNP residues 195-1084
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum FcB1/Columbia (eukaryote)
Plasmid: PTRCHIS-2B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Non-polymers , 6 types, 856 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-R5X / 3-amino-N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}benzamide


Mass: 351.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17N5O3
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 844 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% (v/v) PEG 8000, 10* (v/v) glycerol, 0.1 M Tris pH 8.5, 0.2 M MgCl2, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 13, 2013
RadiationMonochromator: DOUBLE CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→46.39 Å / Num. obs: 83514 / % possible obs: 100 % / Redundancy: 61.2 % / Biso Wilson estimate: 21.58 Å2 / Rmerge(I) obs: 0.356 / Net I/σ(I): 35.9 / Scaling rejects: 31969
Reflection shell

Rmerge(I) obs: 0.038 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
1.85-1.8961.32.42904804738100
9.43-46.3948.9255.63583073299.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.2.4data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→46.39 Å / FOM work R set: 0.8766 / SU ML: 0.2 / σ(F): 1.33 / Phase error: 19.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2041 4224 5.06 %
Rwork0.1622 --
obs0.1644 83420 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.08 Å2 / Biso mean: 28.55 Å2 / Biso min: 9.28 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7177 0 72 844 8093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097434
X-RAY DIFFRACTIONf_angle_d1.13210067
X-RAY DIFFRACTIONf_chiral_restr0.0491112
X-RAY DIFFRACTIONf_plane_restr0.0061283
X-RAY DIFFRACTIONf_dihedral_angle_d13.7672760
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.8710.2931280.245325902718
1.871-1.8930.31871430.256326302773
1.893-1.91610.28731200.214326182738
1.9161-1.94040.25731590.203125782737
1.9404-1.96590.21621420.189926072749
1.9659-1.99280.21891260.184826282754
1.9928-2.02130.22881360.1826052741
2.0213-2.05150.25011470.182425912738
2.0515-2.08350.22371570.178426202777
2.0835-2.11770.21181550.175426082763
2.1177-2.15420.21251410.168325982739
2.1542-2.19340.23231560.16326042760
2.1934-2.23560.23251230.164526252748
2.2356-2.28120.21771340.167426452779
2.2812-2.33080.25881340.16826462780
2.3308-2.3850.21231390.162725992738
2.385-2.44470.21781240.160326362760
2.4447-2.51080.2011530.161926262779
2.5108-2.58460.20981430.157526342777
2.5846-2.66810.21551360.162726312767
2.6681-2.76340.19161410.163426452786
2.7634-2.8740.21131470.161126382785
2.874-3.00480.22841390.159826482787
3.0048-3.16320.1931320.166126742806
3.1632-3.36130.22261430.155426372780
3.3613-3.62080.17681220.147426892811
3.6208-3.9850.16561560.14826802836
3.985-4.56120.16961280.134727182846
4.5612-5.74490.17121480.145727232871
5.7449-46.4050.1881720.168228252997
Refinement TLS params.Method: refined / Origin x: 17.7558 Å / Origin y: 3.6768 Å / Origin z: 10.1625 Å
111213212223313233
T0.1213 Å2-0.0043 Å20.0081 Å2-0.1302 Å20.0139 Å2--0.1203 Å2
L0.5244 °2-0.1838 °20.0573 °2-1.1506 °20.3737 °2--0.8774 °2
S-0.0846 Å °-0.0337 Å °0.0531 Å °-0.0017 Å °0.0173 Å °0.006 Å °-0.1212 Å °-0.0079 Å °0.054 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA197 - 1084
2X-RAY DIFFRACTION1allA1 - 1101
3X-RAY DIFFRACTION1allA1 - 1102
4X-RAY DIFFRACTION1allA2 - 1103
5X-RAY DIFFRACTION1allA3 - 1104
6X-RAY DIFFRACTION1allA1 - 1105
7X-RAY DIFFRACTION1allA1 - 1106
8X-RAY DIFFRACTION1allA1 - 2044
9X-RAY DIFFRACTION1allA1 - 1107
10X-RAY DIFFRACTION1allA1 - 1112

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